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Displaying 1-15 out of 15 total
Auto-Pipe: Streaming Applications on Architecturally Diverse Systems
Found in: Computer
By Roger D. Chamberlain, Mark A. Franklin, Eric J. Tyson, James H. Buckley, Jeremy Buhler, Greg Galloway, Saurabh Gayen, Michael Hall, E.F. Berkley Shands, Naveen Singla
Issue Date:March 2010
pp. 42-49
No summary available.
 
Accelerating Nussinov RNA secondary structure prediction with systolic arrays on FPGAs
Found in: Application-Specific Systems, Architectures and Processors, IEEE International Conference on
By Arpith Jacob, Jeremy Buhler, Roger D. Chamberlain
Issue Date:July 2008
pp. 191-196
RNA structure prediction, or folding, is a compute-intensive task that lies at the core of several search applications in bioinformatics. We begin to address the need for high-throughput RNA folding by accelerating the Nussinov folding algorithm using a 2D...
 
Designing Patterns and Profiles for Faster HMM Search
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Yanni Sun, Jeremy Buhler
Issue Date:April 2009
pp. 232-243
Profile HMMs are powerful tools for modeling conserved motifs in proteins. They are widely used by search tools to classify new protein sequences into families based on domain architecture. However, the proliferation of known motifs and new proteomic seque...
 
Application development on hybrid systems
Found in: SC Conference
By Roger D. Chamberlain, Mark A. Franklin, Eric J. Tyson, Jeremy Buhler, Saurabh Gayen, Patrick Crowley, James H. Buckley
Issue Date:November 2007
pp. 1-10
Hybrid systems consisting of a multitude of different computing device types are interesting targets for high-performance applications. Chip multiprocessors, FPGAs, DSPs, and GPUs can be readily put together into a hybrid system; however, it is not at all ...
 
FPGA-accelerated seed generation in Mercury BLASTP
Found in: Field-Programmable Custom Computing Machines, Annual IEEE Symposium on
By Arpith Jacob, Joseph Lancaster, Jeremy Buhler, Roger D. Chamberlain
Issue Date:April 2007
pp. 95-106
BLASTP is the most popular tool for comparative analysis of protein sequences. In recent years, an exponential increase in the size of protein sequence databases has required either exponentially more runtime or a cluster of machines to keep pace. To addre...
 
Scalable Softcore Vector Processor for Biosequence Applications
Found in: Field-Programmable Custom Computing Machines, Annual IEEE Symposium on
By Arpith C. Jacob, Brandon Harris, Jeremy Buhler, Roger Chamberlain, Young H. Cho
Issue Date:April 2006
pp. 295-296
<p>Currently available genome databases are growing exponentially in size1, making it difficult for software analysis tools to keep up. A number of hardware accelerators utilizing special purpose VLSI [1] or reconfigurable hardware [2] have been prop...
 
Exploiting Coarse-Grained Parallelism to Accelerate Protein Motif Finding with a Network Processor
Found in: Parallel Architectures and Compilation Techniques, International Conference on
By Ben Wun, Jeremy Buhler, Patrick Crowley
Issue Date:September 2005
pp. 173-184
<p>While general-purpose processors have only recently employed chip multiprocessor (CMP) architectures, network processors (NPs) have used heterogeneous multi-core architectures since the late 1990s. NPs differ qualitatively from workstation and ser...
 
Biosequence Similarity Search on the Mercury System
Found in: Application-Specific Systems, Architectures and Processors, IEEE International Conference on
By Praveen Krishnamurthy, Jeremy Buhler, Roger Chamberlain, Mark Franklin, Kwame Gyang, Joseph Lancaster
Issue Date:September 2004
pp. 365-375
Biosequence similarity search is an important application in modern molecular biology. Search algorithms aim to identify sets of sequences whose extensional similarity suggests a common evolutionary origin or function. The most widely used similarity searc...
 
Designing Patterns and Profiles for Faster HMM Search
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Jeremy Buhler, Yanni Sun
Issue Date:April 2009
pp. 232-243
Profile HMMs are powerful tools for modeling conserved motifs in proteins. They are widely used by search tools to classify new protein sequences into families based on domain architecture. However, the proliferation of known motifs and new proteomic seque...
     
Mercury BLASTP: Accelerating Protein Sequence Alignment
Found in: ACM Transactions on Reconfigurable Technology and Systems (TRETS)
By Arpith Jacob, Brandon Harris, Jeremy Buhler, Joseph Lancaster, Roger D. Chamberlain
Issue Date:June 2008
pp. 1-44
Large-scale protein sequence comparison is an important but compute-intensive task in molecular biology. BLASTP is the most popular tool for comparative analysis of protein sequences. In recent years, an exponential increase in the size of protein sequence...
     
Application development on hybrid systems
Found in: Proceedings of the 2007 ACM/IEEE conference on Supercomputing (SC '07)
By Eric J. Tyson, James H. Buckley, Jeremy Buhler, Mark A. Franklin, Patrick Crowley, Roger D. Chamberlain, Saurabh Gayen
Issue Date:November 2007
pp. 24-31
Hybrid systems consisting of a multitude of different computing device types are interesting targets for high-performance applications. Chip multiprocessors, FPGAs, DSPs, and GPUs can be readily put together into a hybrid system; however, it is not at all ...
     
Designing seeds for similarity search in genomic DNA
Found in: Proceedings of the seventh annual international conference on Computational molecular biology (RECOMB '03)
By Jeremy Buhler, Uri Keich, Yanni Sun
Issue Date:April 2003
pp. 67-75
Large-scale comparison of genomic DNA is of fundamental importance in annotating functional elements of genomes. To perform large comparisons e.ciently, BLAST [3, 2] and other widely used tools use seeded alignment, which compares only sequences that can b...
     
Provably sensitive Indexing strategies for biosequence similarity search
Found in: Proceedings of the sixth annual international conference on Computational biology (RECOMB '02)
By Jeremy Buhler
Issue Date:April 2002
pp. 90-99
The field of algorithms for pairwise biosequence similarity search is dominated by heuristic methods of high efficiency but uncertain sensitivity. One reason that more formal string matching algorithms with sensitivity guarantees have not been applied to b...
     
Finding motifs using random projections
Found in: Proceedings of the fifth annual international conference on Computational biology (RECOMB '01)
By Jeremy Buhler, Martin Tompa
Issue Date:April 2001
pp. 69-76
Pevzner and Sze [23] considered a precise version of the motif discovery problem and simultaneously issued an algorithmic challenge: find a motif M of length 15, where each planted instance differs from M in 4 positions. Whereas previous algorithms all fai...
     
The Fox Project: a language-structured approach to networking software
Found in: Crossroads
By Jeremy Buhler
Issue Date:September 1994
pp. 12-18
Its potential sounds so appealing, but there are several challenges to overcome before true ubiquitous computing will garner global acceptance.
     
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